PinkIndexer broken with refinement types 4 and 5
I got a bug report from someone, which I was quickly able to reproduce on an unrelated dataset.
With --pinkindexer-refinement-type=4:
[I] taw@aeolian ~/e/5HT2B> ./run-indexing
WARNING: You did not specify --int-radius.
WARNING: I will use the default values, which are probably not appropriate for your patterns.
This is what I understood your unit cell to be:
orthorhombic C, unique axis ?, right handed.
a b c alpha beta gamma
61.40 122.60 168.00 A 90.00 90.00 90.00 deg
List of indexing methods:
0: pinkIndexer-nolatt-cell (pinkIndexer using cell parameters as prior information)
Indexing parameters:
Check unit cell parameters: on
Check peak alignment: on
Refine indexing solutions: on
Multi-lattice indexing ("delete and retry"): off
Retry indexing: on
peak count used for indexing: 28
computed 0%
Waiting for the last patterns to be processed...
computed 57.1429%
indexamajig: /usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:408: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator[](Eigen::Index) [with Derived = Eigen::Array<float, -1, 1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = float; Eigen::Index = long int]: Assertion `index >= 0 && index < size()' failed.
0 images processed, 0 hits (-nan%), 0 indexable (-nan% of hits, -nan% overall), 0 crystals, 0.0 images/sec.
0 images processed, 0 hits (-nan%), 0 indexable (-nan% of hits, -nan% overall), 0 crystals, 0.0 images/sec.
Worker 0 was killed by signal 6
Event ID was: cxidb-21-run0135/data1/LCLS_2013_Mar23_r0135_015729_c66f.h5 // 1
Task ID was: indexing:pinkindexer
Final: 0 images processed, 0 hits (-nan%), 0 indexable (-nan% of hits, -nan% overall), 0 crystals.
[I] taw@aeolian ~/e/5HT2B [5]> vim run-indexing
With --pinkindexer-refinement-type=3 (retry enabled):
[I] taw@aeolian ~/e/5HT2B> ./run-indexing
WARNING: You did not specify --int-radius.
WARNING: I will use the default values, which are probably not appropriate for your patterns.
This is what I understood your unit cell to be:
orthorhombic C, unique axis ?, right handed.
a b c alpha beta gamma
61.40 122.60 168.00 A 90.00 90.00 90.00 deg
List of indexing methods:
0: pinkIndexer-nolatt-cell (pinkIndexer using cell parameters as prior information)
Indexing parameters:
Check unit cell parameters: on
Check peak alignment: on
Refine indexing solutions: on
Multi-lattice indexing ("delete and retry"): off
Retry indexing: on
peak count used for indexing: 28
computed 0%
Waiting for the last patterns to be processed...
computed 57.1429%
peak count used for indexing: 26
computed 0%
computed 61.5385%
peak count used for indexing: 24
computed 0%
0 images processed, 0 hits (-nan%), 0 indexable (-nan% of hits, -nan% overall), 0 crystals, 0.0 images/sec.
computed 66.6667%
peak count used for indexing: 22
computed 0%
computed 72.7273%
peak count used for indexing: 20
computed 0%
computed 80%
peak count used for indexing: 18
computed 0%
0 images processed, 0 hits (-nan%), 0 indexable (-nan% of hits, -nan% overall), 0 crystals, 0.0 images/sec.
computed 88.8889%
Final: 1 images processed, 1 hits (100.0%), 0 indexable (0.0% of hits, 0.0% overall), 0 crystals.